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Table 1 Reference genomes used in this study

From: Combining multiple functional annotation tools increases coverage of metabolic annotation

Genome Name Biocyc ID Phylum NCBI Accessions Proteins
Mycobacterium tuberculosis CDC1551 MTBCDC1551 Actinobacteria AE000516 4189
Mycobacterium tuberculosis H37Rv MTBH37RV Actinobacteria AL123456 4018
Streptomyces coelicolor A3(2) SCO Actinobacteria NC_003888, NC_003903, NC_003904 8152
Bacteroides thetaiotaomicron VPI-5482 BTHE Bacteroidetes AE015928, AY171301 4825
Candidatus Cardinium hertigiib CBTQ1 Bacteroidetes HG422566, CBQZ010000001- CBQZ010000011 739
Synechococcus elongatus PCC 7942 SYNEL Cyanobacteria CP000100, CP000101 2661
Listeria monocytogenes 10403S 10403S_RAST Firmicutes CP002002 2814
Bacillus anthracis Ames ANTHRA Firmicutes NC_003997, AE017335, AE017336 5602
Bacillus subtilis 168 BSUB Firmicutes AL009126 4185
Clostridium saccharoperbutylacetonicum ATCC 27021 CLOSSAC Firmicutes CP004121, CP004122 5821
Eubacterium rectale ATCC 33656 EREC Firmicutes CP001107 3626
Clostridioides difficile 630 PDIF272563 Firmicutes AM180355, AM180356 3809
Agrobacterium fabrum C58 AGRO Proteobacteria AE008687, AE008688, AE008689, AE008690 5402
Aurantimonas manganoxydans SI85-9A1 AURANTIMONAS Proteobacteria AAPJ01000001- AAPJ01000035 3650
Caulobacter crescentus CB15 CAULO Proteobacteria AE005673 3737
Caulobacter crescentus NA1000 CAULONA1000 Proteobacteria CP001340 3885
Escherichia coli CFT073 ECOL199310 Proteobacteria AE014075 5379
Escherichia coli K-12 substr. W3110 ECOL316407 Proteobacteria NC_007779 4410
Escherichia coli B str. REL606 ECOL413997 Proteobacteria CP000819 4209
Escherichia coli K-12 substr. MG1655a ECOLI Proteobacteria U00096 4140
Escherichia coli O157:H7 str. EDL933 ECO0157 Proteobacteria AE005174, AF074613 5449
Candidatus Evansia muellerib EVA Proteobacteria LM655252 330
Helicobacter pylori 26,695 HPY Proteobacteria CP003904 1594
Methylosinus trichosporium OB3b MOB3B Proteobacteria NZ_ADVE02000001- NZ_ADVE02000003 4344
Candidatus Portiera aleyrodidarum BT-QVLCb PABTQVLC Proteobacteria CP003867 280
Shigella flexneri 2a str. 2457 T SHIGELLA Proteobacteria AE014073 4068
Vibrio cholerae O1 biovar El Tor str. N16961 VCHO Proteobacteria AE003852, AE003853 3828
  1. aTier 1 Pathway Genome Database (EcoCyc)
  2. bEndosymbiont with reduced genome